# ##################################################################################################
#  Disclaimer                                                                                      #
#  This file is a python3 translation of AutoDockTools (v.1.5.7)                                   #
#  Modifications made by Valdes-Tresanco MS (https://github.com/Valdes-Tresanco-MS)                #
#  Tested by Valdes-Tresanco-MS and Valdes-Tresanco ME                                             #
#  There is no guarantee that it works like the original distribution,                             #
#  but feel free to tell us if you get any difference to correct the code.                         #
#                                                                                                  #
#  Please use this cite the original reference.                                                    #
#  If you think my work helps you, just keep this note intact on your program.                     #
#                                                                                                  #
#  Modification date: 10/5/20 18:51                                                                #
#                                                                                                  #
# ##################################################################################################

#############################################################################
#
# Author: Ruth HUEY, William LINDSTROM
#
# Copyright: M. Sanner TSRI 2000
#
#############################################################################

# $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/energyConstants.py,v 1.4 2002/03/12 21:24:55 rhuey Exp $
#
#
# $Id: energyConstants.py,v 1.4 2002/03/12 21:24:55 rhuey Exp $
#
#


# FROM constants.py
# from: gpf3gen 
# Free energy model 140n s coefficients:
#
FE_vdW_coeff = 0.1485
FE_estat_coeff = 0.1146
FE_hbond_coeff = 0.0656
FE_tors_coeff = 0.3113
FE_desol_coeff = 0.1711

# AutoDock Binding Free Energy Model 140n
# Uses the C.A.Lig.only solvation model, i.e.
# aliphatic (C) and aromatic (A) carbon atoms only
#
SolVol = {}
SolVol["C"] = 12.77
SolVol["A"] = 10.80
SolVol["N"] = 0.
SolVol["n"] = 0.
SolVol["O"] = 0.
SolVol["H"] = 0.

# SolPar[ "C" ] =  0.6844
# SolPar[ "A" ] =  0.1027

SolPar = {}
SolPar["C"] = 4.0 * FE_desol_coeff
SolPar["A"] = 0.6 * FE_desol_coeff
SolPar["N"] = 0.
SolPar["n"] = 0.
SolPar["O"] = 0.
SolPar["H"] = 0.

SolCon = {}
SolCon["C"] = 0.
SolCon["A"] = 0.
SolCon["N"] = 0.
SolCon["n"] = 0.
SolCon["O"] = 0.236
SolCon["H"] = 0.118

Rij = {}
Rij["lj" "C" "C"] = 4.00
Rij["lj" "C" "N"] = 3.75
Rij["lj" "C" "n"] = 3.75
Rij["lj" "C" "O"] = 3.60
Rij["lj" "C" "P"] = 4.10
Rij["lj" "C" "S"] = 4.00
Rij["lj" "C" "H"] = 3.00
Rij["lj" "C" "f"] = 2.65
Rij["lj" "C" "F"] = 3.54
Rij["lj" "C" "c"] = 4.04
Rij["lj" "C" "b"] = 4.17
Rij["lj" "C" "I"] = 4.36
# Rij[ "lj" "C" "M" ] = 2.79
Rij["lj" "C" "M"] = 2.65  # Mg
Rij["lj" "C" "Z"] = 2.74  # Zn
Rij["lj" "C" "L"] = 2.99  # Ca
Rij["lj" "C" "X"] = 3.00  # Xx

Rij["lj" "N" "C"] = 3.75
Rij["lj" "N" "N"] = 3.50
Rij["lj" "N" "n"] = 3.50
Rij["lj" "N" "O"] = 3.35
Rij["lj" "N" "P"] = 3.85
Rij["lj" "N" "S"] = 3.75
Rij["lj" "N" "H"] = 2.75
Rij["lj" "N" "f"] = 2.40
Rij["lj" "N" "F"] = 3.29
Rij["lj" "N" "c"] = 3.79
Rij["lj" "N" "b"] = 3.92
Rij["lj" "N" "I"] = 4.11
# Rij[ "lj" "N" "M" ] = 2.54
Rij["lj" "N" "M"] = 2.40  # Mg
Rij["lj" "N" "Z"] = 2.49  # Zn
Rij["lj" "N" "L"] = 2.74  # Ca
Rij["lj" "N" "X"] = 2.75  # Xx

Rij["lj" "n" "C"] = 3.75
Rij["lj" "n" "N"] = 3.50
Rij["lj" "n" "n"] = 3.50
Rij["lj" "n" "O"] = 3.35
Rij["lj" "n" "P"] = 3.85
Rij["lj" "n" "S"] = 3.75
Rij["lj" "n" "H"] = 2.75
Rij["lj" "n" "f"] = 2.40
Rij["lj" "n" "F"] = 3.29
Rij["lj" "n" "c"] = 3.79
Rij["lj" "n" "b"] = 3.92
Rij["lj" "n" "I"] = 4.11
# Rij[ "lj" "n" "M" ] = 2.54
Rij["lj" "n" "M"] = 2.40  # Mg
Rij["lj" "n" "Z"] = 2.49  # Zn
Rij["lj" "n" "L"] = 2.74  # Ca
Rij["lj" "n" "X"] = 2.75  # Xx

Rij["lj" "O" "C"] = 3.60
Rij["lj" "O" "N"] = 3.35
Rij["lj" "O" "n"] = 3.35
Rij["lj" "O" "O"] = 3.20
Rij["lj" "O" "P"] = 3.70
Rij["lj" "O" "S"] = 3.60
Rij["lj" "O" "H"] = 2.60
Rij["lj" "O" "f"] = 2.25
Rij["lj" "O" "F"] = 3.15
Rij["lj" "O" "c"] = 3.65
Rij["lj" "O" "b"] = 3.77
Rij["lj" "O" "I"] = 3.96
# Rij[ "lj" "O" "M" ] = 2.39
Rij["lj" "O" "M"] = 2.25  # Mg
Rij["lj" "O" "Z"] = 2.34  # Zn
Rij["lj" "O" "L"] = 2.59  # Ca
Rij["lj" "O" "X"] = 2.60  # Xx

Rij["lj" "P" "C"] = 4.10
Rij["lj" "P" "N"] = 3.85
Rij["lj" "P" "n"] = 3.85
Rij["lj" "P" "O"] = 3.70
Rij["lj" "P" "P"] = 4.20
Rij["lj" "P" "S"] = 4.10
Rij["lj" "P" "H"] = 3.10
Rij["lj" "P" "f"] = 2.75
Rij["lj" "P" "F"] = 3.65
Rij["lj" "P" "c"] = 4.14
Rij["lj" "P" "b"] = 4.27
Rij["lj" "P" "I"] = 4.46
# Rij[ "lj" "P" "M" ] = 2.89
Rij["lj" "P" "M"] = 2.75  # Mg
Rij["lj" "P" "Z"] = 2.84  # Zn
Rij["lj" "P" "L"] = 3.09  # Ca
Rij["lj" "P" "X"] = 3.10  # Xx

Rij["lj" "S" "C"] = 4.00
Rij["lj" "S" "N"] = 3.75
Rij["lj" "S" "n"] = 3.75
Rij["lj" "S" "O"] = 3.60
Rij["lj" "S" "P"] = 4.10
Rij["lj" "S" "S"] = 4.00
Rij["lj" "S" "H"] = 3.00
Rij["lj" "S" "f"] = 2.65
Rij["lj" "S" "F"] = 3.54
Rij["lj" "S" "c"] = 4.04
Rij["lj" "S" "b"] = 4.17
Rij["lj" "S" "I"] = 4.36
# Rij[ "lj" "S" "M" ] = 2.79
Rij["lj" "S" "M"] = 2.65  # Mg
Rij["lj" "S" "Z"] = 2.74  # Zn
Rij["lj" "S" "L"] = 2.99  # Ca
Rij["lj" "S" "X"] = 3.00  # Xx

Rij["lj" "H" "C"] = 3.00
Rij["lj" "H" "N"] = 2.75
Rij["lj" "H" "n"] = 2.75
Rij["lj" "H" "O"] = 2.60
Rij["lj" "H" "P"] = 3.10
Rij["lj" "H" "S"] = 3.00
Rij["lj" "H" "H"] = 2.00
Rij["lj" "H" "f"] = 1.65
Rij["lj" "H" "F"] = 2.54
Rij["lj" "H" "c"] = 3.04
Rij["lj" "H" "b"] = 3.17
Rij["lj" "H" "I"] = 3.36
# Rij[ "lj" "H" "M" ] = 1.79
Rij["lj" "H" "M"] = 1.65  # Mg
Rij["lj" "H" "Z"] = 1.74  # Zn
Rij["lj" "H" "L"] = 1.99  # Ca
Rij["lj" "H" "X"] = 2.00  # Xx

Rij["lj" "f" "C"] = 2.65
Rij["lj" "f" "N"] = 2.40
Rij["lj" "f" "n"] = 2.40
Rij["lj" "f" "O"] = 2.25
Rij["lj" "f" "P"] = 2.75
Rij["lj" "f" "S"] = 2.65
Rij["lj" "f" "H"] = 1.65
Rij["lj" "f" "f"] = 1.30
Rij["lj" "f" "F"] = 2.19
Rij["lj" "f" "c"] = 2.69
Rij["lj" "f" "b"] = 2.81
Rij["lj" "f" "I"] = 3.01
# Rij[ "lj" "f" "M" ] = 1.44
Rij["lj" "f" "M"] = 1.30  # Mg
Rij["lj" "f" "Z"] = 1.39  # Zn
Rij["lj" "f" "L"] = 1.64  # Ca
Rij["lj" "f" "X"] = 1.65  # Xx

Rij["lj" "F" "C"] = 3.54
Rij["lj" "F" "N"] = 3.29
Rij["lj" "F" "n"] = 3.29
Rij["lj" "F" "O"] = 3.15
Rij["lj" "F" "P"] = 3.65
Rij["lj" "F" "S"] = 3.54
Rij["lj" "F" "H"] = 2.54
Rij["lj" "F" "f"] = 2.19
Rij["lj" "F" "F"] = 3.09
Rij["lj" "F" "c"] = 3.59
Rij["lj" "F" "b"] = 3.71
Rij["lj" "F" "I"] = 3.90
# Rij[ "lj" "F" "M" ] = 2.33
Rij["lj" "F" "M"] = 2.19  # Mg
Rij["lj" "F" "Z"] = 2.29  # Zn
Rij["lj" "F" "L"] = 2.54  # Ca
Rij["lj" "F" "X"] = 2.54  # Xx

Rij["lj" "c" "C"] = 4.04
Rij["lj" "c" "N"] = 3.79
Rij["lj" "c" "n"] = 3.79
Rij["lj" "c" "O"] = 3.65
Rij["lj" "c" "P"] = 4.14
Rij["lj" "c" "S"] = 4.04
Rij["lj" "c" "H"] = 3.04
Rij["lj" "c" "f"] = 2.69
Rij["lj" "c" "F"] = 3.59
Rij["lj" "c" "c"] = 4.09
Rij["lj" "c" "b"] = 4.21
Rij["lj" "c" "I"] = 4.40
# Rij[ "lj" "c" "M" ] = 2.83
Rij["lj" "c" "M"] = 2.69  # Mg
Rij["lj" "c" "Z"] = 2.79  # Zn
Rij["lj" "c" "L"] = 3.04  # Ca
Rij["lj" "c" "X"] = 3.04  # Xx

Rij["lj" "b" "C"] = 4.17
Rij["lj" "b" "N"] = 3.92
Rij["lj" "b" "n"] = 3.92
Rij["lj" "b" "O"] = 3.77
Rij["lj" "b" "P"] = 4.27
Rij["lj" "b" "S"] = 4.17
Rij["lj" "b" "H"] = 3.17
Rij["lj" "b" "f"] = 2.81
Rij["lj" "b" "F"] = 3.71
Rij["lj" "b" "c"] = 4.21
Rij["lj" "b" "b"] = 4.33
Rij["lj" "b" "I"] = 4.53
# Rij[ "lj" "b" "M" ] = 2.95
Rij["lj" "b" "M"] = 2.81  # Mg
Rij["lj" "b" "Z"] = 2.91  # Zn
Rij["lj" "b" "L"] = 3.16  # Ca
Rij["lj" "b" "X"] = 3.17  # Xx

Rij["lj" "I" "C"] = 4.36
Rij["lj" "I" "N"] = 4.11
Rij["lj" "I" "n"] = 4.11
Rij["lj" "I" "O"] = 3.96
Rij["lj" "I" "P"] = 4.46
Rij["lj" "I" "S"] = 4.36
Rij["lj" "I" "H"] = 3.36
Rij["lj" "I" "f"] = 3.01
Rij["lj" "I" "F"] = 3.90
Rij["lj" "I" "c"] = 4.40
Rij["lj" "I" "b"] = 4.53
Rij["lj" "I" "I"] = 4.72
# Rij[ "lj" "I" "M" ] = 3.15
Rij["lj" "I" "M"] = 3.01  # Mg
Rij["lj" "I" "Z"] = 3.10  # Zn
Rij["lj" "I" "L"] = 3.35  # Ca
Rij["lj" "I" "X"] = 3.36  # Xx

# Rij[ "lj" "M" "C" ] = 2.79
# Rij[ "lj" "M" "N" ] = 2.54
# Rij[ "lj" "M" "n" ] = 2.54
# Rij[ "lj" "M" "O" ] = 2.39
# Rij[ "lj" "M" "P" ] = 2.89
# Rij[ "lj" "M" "S" ] = 2.79
# Rij[ "lj" "M" "H" ] = 1.79
# Rij[ "lj" "M" "f" ] = 1.44
# Rij[ "lj" "M" "F" ] = 2.33
# Rij[ "lj" "M" "c" ] = 2.83
# Rij[ "lj" "M" "b" ] = 2.95
# Rij[ "lj" "M" "I" ] = 3.15
# Rij[ "lj" "M" "M" ] = 1.57

# Mg
Rij["lj" "M" "C"] = 2.65
Rij["lj" "M" "N"] = 2.40
Rij["lj" "M" "n"] = 2.40
Rij["lj" "M" "O"] = 2.25
Rij["lj" "M" "P"] = 2.75
Rij["lj" "M" "S"] = 2.65
Rij["lj" "M" "H"] = 1.65
Rij["lj" "M" "f"] = 1.30
Rij["lj" "M" "F"] = 2.19
Rij["lj" "M" "c"] = 2.69
Rij["lj" "M" "b"] = 2.81
Rij["lj" "M" "I"] = 3.01
Rij["lj" "M" "M"] = 1.30  # Mg
Rij["lj" "M" "Z"] = 1.39  # Zn
Rij["lj" "M" "L"] = 1.64  # Ca
Rij["lj" "M" "X"] = 1.65  # Xx

# Zn
Rij["lj" "Z" "C"] = 2.74
Rij["lj" "Z" "N"] = 2.49
Rij["lj" "Z" "n"] = 2.49
Rij["lj" "Z" "O"] = 2.34
Rij["lj" "Z" "P"] = 2.84
Rij["lj" "Z" "S"] = 2.74
Rij["lj" "Z" "H"] = 1.74
Rij["lj" "Z" "f"] = 1.39
Rij["lj" "Z" "F"] = 2.29
Rij["lj" "Z" "c"] = 2.79
Rij["lj" "Z" "b"] = 2.91
Rij["lj" "Z" "I"] = 3.10
Rij["lj" "Z" "M"] = 1.39  # Mg
Rij["lj" "Z" "Z"] = 1.48  # Zn
Rij["lj" "Z" "L"] = 1.73  # Ca
Rij["lj" "Z" "X"] = 1.74  # Xx

# Ca
Rij["lj" "L" "C"] = 2.99
Rij["lj" "L" "N"] = 2.74
Rij["lj" "L" "n"] = 2.74
Rij["lj" "L" "O"] = 2.59
Rij["lj" "L" "P"] = 3.09
Rij["lj" "L" "S"] = 2.99
Rij["lj" "L" "H"] = 1.99
Rij["lj" "L" "f"] = 1.64
Rij["lj" "L" "F"] = 2.54
Rij["lj" "L" "c"] = 3.04
Rij["lj" "L" "b"] = 3.16
Rij["lj" "L" "I"] = 3.35
Rij["lj" "L" "M"] = 1.64  # Mg
Rij["lj" "L" "Z"] = 1.73  # Zn
Rij["lj" "L" "L"] = 1.98  # Ca
Rij["lj" "L" "X"] = 1.99  # Xx

# Xx
Rij["lj" "X" "C"] = 3.00
Rij["lj" "X" "N"] = 2.75
Rij["lj" "X" "n"] = 2.75
Rij["lj" "X" "O"] = 2.60
Rij["lj" "X" "P"] = 3.10
Rij["lj" "X" "S"] = 3.00
Rij["lj" "X" "H"] = 2.00
Rij["lj" "X" "f"] = 1.65
Rij["lj" "X" "F"] = 2.54
Rij["lj" "X" "c"] = 3.04
Rij["lj" "X" "b"] = 3.17
Rij["lj" "X" "I"] = 3.36
Rij["lj" "X" "M"] = 1.65  # Mg
Rij["lj" "X" "Z"] = 1.74  # Zn
Rij["lj" "X" "L"] = 1.99  # Ca
Rij["lj" "X" "X"] = 2.00  # Xx

# A:aromatic carbon
Rij["lj" "C" "A"] = Rij["lj" "C" "C"]
Rij["lj" "A" "C"] = Rij["lj" "C" "A"]
Rij["lj" "A" "A"] = Rij["lj" "C" "C"]

Rij["lj" "A" "N"] = Rij["lj" "C" "N"]
Rij["lj" "A" "n"] = Rij["lj" "C" "n"]
Rij["lj" "A" "O"] = Rij["lj" "C" "O"]
Rij["lj" "A" "S"] = Rij["lj" "C" "S"]
Rij["lj" "A" "H"] = Rij["lj" "C" "H"]
Rij["lj" "A" "P"] = Rij["lj" "C" "P"]
Rij["lj" "A" "f"] = Rij["lj" "C" "f"]
Rij["lj" "A" "F"] = Rij["lj" "C" "F"]
Rij["lj" "A" "c"] = Rij["lj" "C" "c"]
Rij["lj" "A" "b"] = Rij["lj" "C" "b"]
Rij["lj" "A" "I"] = Rij["lj" "C" "I"]
Rij["lj" "A" "M"] = Rij["lj" "C" "M"]
Rij["lj" "A" "Z"] = Rij["lj" "C" "Z"]
Rij["lj" "A" "L"] = Rij["lj" "C" "L"]
Rij["lj" "A" "X"] = Rij["lj" "C" "X"]

Rij["lj" "N" "A"] = Rij["lj" "A" "N"]
Rij["lj" "n" "A"] = Rij["lj" "A" "n"]
Rij["lj" "O" "A"] = Rij["lj" "A" "O"]
Rij["lj" "S" "A"] = Rij["lj" "A" "S"]
Rij["lj" "H" "A"] = Rij["lj" "A" "H"]
Rij["lj" "P" "A"] = Rij["lj" "A" "P"]
Rij["lj" "f" "A"] = Rij["lj" "A" "f"]
Rij["lj" "F" "A"] = Rij["lj" "A" "F"]
Rij["lj" "c" "A"] = Rij["lj" "A" "c"]
Rij["lj" "b" "A"] = Rij["lj" "A" "b"]
Rij["lj" "I" "A"] = Rij["lj" "A" "I"]
Rij["lj" "M" "A"] = Rij["lj" "A" "M"]
Rij["lj" "Z" "A"] = Rij["lj" "A" "Z"]
Rij["lj" "L" "A"] = Rij["lj" "A" "M"]
Rij["lj" "X" "A"] = Rij["lj" "A" "X"]

#
# AutoDock Binding Free Energy Model 140n
# New well-depths using new Solvation Model, 
# multiplied by van der Waals coefficient, 0.1485
#

#
# Well-depths prior to Solvation Model, multiplied by FE_vdW_coeff
#
epsij = {}
epsij["lj" "C" "C"] = 0.1500 * FE_vdW_coeff
epsij["lj" "C" "N"] = 0.1549 * FE_vdW_coeff
epsij["lj" "C" "n"] = 0.1549 * FE_vdW_coeff
epsij["lj" "C" "O"] = 0.1732 * FE_vdW_coeff
epsij["lj" "C" "P"] = 0.1732 * FE_vdW_coeff
epsij["lj" "C" "S"] = 0.1732 * FE_vdW_coeff
epsij["lj" "C" "H"] = 0.0548 * FE_vdW_coeff
epsij["lj" "C" "f"] = 0.0387 * FE_vdW_coeff
epsij["lj" "C" "F"] = 0.1095 * FE_vdW_coeff
epsij["lj" "C" "c"] = 0.2035 * FE_vdW_coeff
epsij["lj" "C" "b"] = 0.2416 * FE_vdW_coeff
epsij["lj" "C" "I"] = 0.2877 * FE_vdW_coeff
# epsij[ "lj" "C" "M" ] = 0.3623 * FE_vdW_coeff
epsij["lj" "C" "M"] = 0.3623 * FE_vdW_coeff
epsij["lj" "C" "Z"] = 0.2872 * FE_vdW_coeff
epsij["lj" "C" "L"] = 0.2872 * FE_vdW_coeff
epsij["lj" "C" "X"] = 0.0548 * FE_vdW_coeff

epsij["lj" "N" "C"] = 0.1549 * FE_vdW_coeff
epsij["lj" "N" "N"] = 0.1600 * FE_vdW_coeff
epsij["lj" "N" "n"] = 0.1600 * FE_vdW_coeff
epsij["lj" "N" "O"] = 0.1789 * FE_vdW_coeff
epsij["lj" "N" "P"] = 0.1789 * FE_vdW_coeff
epsij["lj" "N" "S"] = 0.1789 * FE_vdW_coeff
epsij["lj" "N" "H"] = 0.0566 * FE_vdW_coeff
epsij["lj" "N" "f"] = 0.0400 * FE_vdW_coeff
epsij["lj" "N" "F"] = 0.1131 * FE_vdW_coeff
epsij["lj" "N" "c"] = 0.2101 * FE_vdW_coeff
epsij["lj" "N" "b"] = 0.2495 * FE_vdW_coeff
epsij["lj" "N" "I"] = 0.2972 * FE_vdW_coeff
# epsij[ "lj" "N" "M" ] = 0.3742 * FE_vdW_coeff
epsij["lj" "N" "M"] = 0.3742 * FE_vdW_coeff
epsij["lj" "N" "Z"] = 0.2966 * FE_vdW_coeff
epsij["lj" "N" "L"] = 0.2966 * FE_vdW_coeff
epsij["lj" "N" "X"] = 0.0566 * FE_vdW_coeff

epsij["lj" "n" "C"] = 0.1549 * FE_vdW_coeff
epsij["lj" "n" "N"] = 0.1600 * FE_vdW_coeff
epsij["lj" "n" "n"] = 0.1600 * FE_vdW_coeff
epsij["lj" "n" "O"] = 0.1789 * FE_vdW_coeff
epsij["lj" "n" "P"] = 0.1789 * FE_vdW_coeff
epsij["lj" "n" "S"] = 0.1789 * FE_vdW_coeff
epsij["lj" "n" "H"] = 0.0566 * FE_vdW_coeff
epsij["lj" "n" "f"] = 0.0400 * FE_vdW_coeff
epsij["lj" "n" "F"] = 0.1131 * FE_vdW_coeff
epsij["lj" "n" "c"] = 0.2101 * FE_vdW_coeff
epsij["lj" "n" "b"] = 0.2495 * FE_vdW_coeff
epsij["lj" "n" "I"] = 0.2972 * FE_vdW_coeff
# epsij[ "lj" "n" "M" ] = 0.3742 * FE_vdW_coeff
epsij["lj" "n" "M"] = 0.3742 * FE_vdW_coeff
epsij["lj" "n" "Z"] = 0.2966 * FE_vdW_coeff
epsij["lj" "n" "L"] = 0.2966 * FE_vdW_coeff
epsij["lj" "n" "X"] = 0.0566 * FE_vdW_coeff

epsij["lj" "O" "C"] = 0.1732 * FE_vdW_coeff
epsij["lj" "O" "N"] = 0.1789 * FE_vdW_coeff
epsij["lj" "O" "n"] = 0.1789 * FE_vdW_coeff
epsij["lj" "O" "O"] = 0.2000 * FE_vdW_coeff
epsij["lj" "O" "P"] = 0.2000 * FE_vdW_coeff
epsij["lj" "O" "S"] = 0.2000 * FE_vdW_coeff
epsij["lj" "O" "H"] = 0.0632 * FE_vdW_coeff
epsij["lj" "O" "f"] = 0.0447 * FE_vdW_coeff
epsij["lj" "O" "F"] = 0.1265 * FE_vdW_coeff
epsij["lj" "O" "c"] = 0.2349 * FE_vdW_coeff
epsij["lj" "O" "b"] = 0.2789 * FE_vdW_coeff
epsij["lj" "O" "I"] = 0.3323 * FE_vdW_coeff
# epsij[ "lj" "O" "M" ] = 0.4183 * FE_vdW_coeff
epsij["lj" "O" "M"] = 0.4183 * FE_vdW_coeff
epsij["lj" "O" "Z"] = 0.3317 * FE_vdW_coeff
epsij["lj" "O" "L"] = 0.3317 * FE_vdW_coeff
epsij["lj" "O" "X"] = 0.0632 * FE_vdW_coeff

epsij["lj" "P" "C"] = 0.1732 * FE_vdW_coeff
epsij["lj" "P" "N"] = 0.1789 * FE_vdW_coeff
epsij["lj" "P" "n"] = 0.1789 * FE_vdW_coeff
epsij["lj" "P" "O"] = 0.2000 * FE_vdW_coeff
epsij["lj" "P" "P"] = 0.2000 * FE_vdW_coeff
epsij["lj" "P" "S"] = 0.2000 * FE_vdW_coeff
epsij["lj" "P" "H"] = 0.0632 * FE_vdW_coeff
epsij["lj" "P" "f"] = 0.0447 * FE_vdW_coeff
epsij["lj" "P" "F"] = 0.1265 * FE_vdW_coeff
epsij["lj" "P" "c"] = 0.2349 * FE_vdW_coeff
epsij["lj" "P" "b"] = 0.2789 * FE_vdW_coeff
epsij["lj" "P" "I"] = 0.3323 * FE_vdW_coeff
# epsij[ "lj" "P" "M" ] = 0.4183 * FE_vdW_coeff
epsij["lj" "P" "M"] = 0.4183 * FE_vdW_coeff  # NB: same as O values
epsij["lj" "P" "Z"] = 0.3317 * FE_vdW_coeff
epsij["lj" "P" "L"] = 0.3317 * FE_vdW_coeff
epsij["lj" "P" "X"] = 0.0632 * FE_vdW_coeff

epsij["lj" "S" "C"] = 0.1732 * FE_vdW_coeff
epsij["lj" "S" "N"] = 0.1789 * FE_vdW_coeff
epsij["lj" "S" "n"] = 0.1789 * FE_vdW_coeff
epsij["lj" "S" "O"] = 0.2000 * FE_vdW_coeff
epsij["lj" "S" "P"] = 0.2000 * FE_vdW_coeff
epsij["lj" "S" "S"] = 0.2000 * FE_vdW_coeff
epsij["lj" "S" "H"] = 0.0632 * FE_vdW_coeff
epsij["lj" "S" "f"] = 0.0447 * FE_vdW_coeff
epsij["lj" "S" "F"] = 0.1265 * FE_vdW_coeff
epsij["lj" "S" "c"] = 0.2349 * FE_vdW_coeff
epsij["lj" "S" "b"] = 0.2789 * FE_vdW_coeff
epsij["lj" "S" "I"] = 0.3323 * FE_vdW_coeff
# epsij[ "lj" "S" "M" ] = 0.4183 * FE_vdW_coeff
epsij["lj" "S" "M"] = 0.4183 * FE_vdW_coeff  # NB: same as O values
epsij["lj" "S" "Z"] = 0.3317 * FE_vdW_coeff
epsij["lj" "S" "L"] = 0.3317 * FE_vdW_coeff
epsij["lj" "S" "X"] = 0.0632 * FE_vdW_coeff

epsij["lj" "H" "C"] = 0.0548 * FE_vdW_coeff
epsij["lj" "H" "N"] = 0.0566 * FE_vdW_coeff
epsij["lj" "H" "n"] = 0.0566 * FE_vdW_coeff
epsij["lj" "H" "O"] = 0.0632 * FE_vdW_coeff
epsij["lj" "H" "P"] = 0.0632 * FE_vdW_coeff
epsij["lj" "H" "S"] = 0.0632 * FE_vdW_coeff
epsij["lj" "H" "H"] = 0.0200 * FE_vdW_coeff
epsij["lj" "H" "f"] = 0.0141 * FE_vdW_coeff
epsij["lj" "H" "F"] = 0.0400 * FE_vdW_coeff
epsij["lj" "H" "c"] = 0.0743 * FE_vdW_coeff
epsij["lj" "H" "b"] = 0.0882 * FE_vdW_coeff
epsij["lj" "H" "I"] = 0.1051 * FE_vdW_coeff
# epsij[ "lj" "H" "M" ] = 0.1323 * FE_vdW_coeff
epsij["lj" "H" "M"] = 0.1323 * FE_vdW_coeff
epsij["lj" "H" "Z"] = 0.1049 * FE_vdW_coeff
epsij["lj" "H" "L"] = 0.1049 * FE_vdW_coeff
epsij["lj" "H" "X"] = 0.0200 * FE_vdW_coeff

epsij["lj" "f" "C"] = 0.0387 * FE_vdW_coeff
epsij["lj" "f" "N"] = 0.0400 * FE_vdW_coeff
epsij["lj" "f" "n"] = 0.0400 * FE_vdW_coeff
epsij["lj" "f" "O"] = 0.0447 * FE_vdW_coeff
epsij["lj" "f" "P"] = 0.0447 * FE_vdW_coeff
epsij["lj" "f" "S"] = 0.0447 * FE_vdW_coeff
epsij["lj" "f" "H"] = 0.0141 * FE_vdW_coeff
epsij["lj" "f" "f"] = 0.0100 * FE_vdW_coeff
epsij["lj" "f" "F"] = 0.0283 * FE_vdW_coeff
epsij["lj" "f" "c"] = 0.0525 * FE_vdW_coeff
epsij["lj" "f" "b"] = 0.0624 * FE_vdW_coeff
epsij["lj" "f" "I"] = 0.0743 * FE_vdW_coeff
# epsij[ "lj" "f" "M" ] = 0.0935 * FE_vdW_coeff
epsij["lj" "f" "M"] = 0.0935 * FE_vdW_coeff
epsij["lj" "f" "Z"] = 0.0742 * FE_vdW_coeff
epsij["lj" "f" "L"] = 0.0742 * FE_vdW_coeff
epsij["lj" "f" "X"] = 0.0141 * FE_vdW_coeff

epsij["lj" "F" "C"] = 0.1095 * FE_vdW_coeff
epsij["lj" "F" "N"] = 0.1131 * FE_vdW_coeff
epsij["lj" "F" "n"] = 0.1131 * FE_vdW_coeff
epsij["lj" "F" "O"] = 0.1265 * FE_vdW_coeff
epsij["lj" "F" "P"] = 0.1265 * FE_vdW_coeff
epsij["lj" "F" "S"] = 0.1265 * FE_vdW_coeff
epsij["lj" "F" "H"] = 0.0400 * FE_vdW_coeff
epsij["lj" "F" "f"] = 0.0283 * FE_vdW_coeff
epsij["lj" "F" "F"] = 0.0800 * FE_vdW_coeff
epsij["lj" "F" "c"] = 0.1486 * FE_vdW_coeff
epsij["lj" "F" "b"] = 0.1764 * FE_vdW_coeff
epsij["lj" "F" "I"] = 0.2101 * FE_vdW_coeff
# epsij[ "lj" "F" "M" ] = 0.2646 * FE_vdW_coeff
epsij["lj" "F" "M"] = 0.2646 * FE_vdW_coeff
epsij["lj" "F" "Z"] = 0.2098 * FE_vdW_coeff
epsij["lj" "F" "L"] = 0.2098 * FE_vdW_coeff
epsij["lj" "F" "X"] = 0.0400 * FE_vdW_coeff

epsij["lj" "c" "C"] = 0.2035 * FE_vdW_coeff
epsij["lj" "c" "N"] = 0.2101 * FE_vdW_coeff
epsij["lj" "c" "n"] = 0.2101 * FE_vdW_coeff
epsij["lj" "c" "O"] = 0.2349 * FE_vdW_coeff
epsij["lj" "c" "P"] = 0.2349 * FE_vdW_coeff
epsij["lj" "c" "S"] = 0.2349 * FE_vdW_coeff
epsij["lj" "c" "H"] = 0.0743 * FE_vdW_coeff
epsij["lj" "c" "f"] = 0.0525 * FE_vdW_coeff
epsij["lj" "c" "F"] = 0.1486 * FE_vdW_coeff
epsij["lj" "c" "c"] = 0.2760 * FE_vdW_coeff
epsij["lj" "c" "b"] = 0.3277 * FE_vdW_coeff
epsij["lj" "c" "I"] = 0.3903 * FE_vdW_coeff
# epsij[ "lj" "c" "M" ] = 0.4914 * FE_vdW_coeff
epsij["lj" "c" "M"] = 0.4914 * FE_vdW_coeff
epsij["lj" "c" "Z"] = 0.3896 * FE_vdW_coeff
epsij["lj" "c" "L"] = 0.3896 * FE_vdW_coeff
epsij["lj" "c" "X"] = 0.0743 * FE_vdW_coeff

epsij["lj" "b" "C"] = 0.2416 * FE_vdW_coeff
epsij["lj" "b" "N"] = 0.2495 * FE_vdW_coeff
epsij["lj" "b" "n"] = 0.2495 * FE_vdW_coeff
epsij["lj" "b" "O"] = 0.2789 * FE_vdW_coeff
epsij["lj" "b" "P"] = 0.2789 * FE_vdW_coeff
epsij["lj" "b" "S"] = 0.2789 * FE_vdW_coeff
epsij["lj" "b" "H"] = 0.0882 * FE_vdW_coeff
epsij["lj" "b" "f"] = 0.0624 * FE_vdW_coeff
epsij["lj" "b" "F"] = 0.1764 * FE_vdW_coeff
epsij["lj" "b" "c"] = 0.3277 * FE_vdW_coeff
epsij["lj" "b" "b"] = 0.3890 * FE_vdW_coeff
epsij["lj" "b" "I"] = 0.4634 * FE_vdW_coeff
# epsij[ "lj" "b" "M" ] = 0.5834 * FE_vdW_coeff
epsij["lj" "b" "M"] = 0.5834 * FE_vdW_coeff
epsij["lj" "b" "Z"] = 0.4625 * FE_vdW_coeff
epsij["lj" "b" "L"] = 0.4625 * FE_vdW_coeff
epsij["lj" "b" "X"] = 0.0882 * FE_vdW_coeff

epsij["lj" "I" "C"] = 0.2877 * FE_vdW_coeff
epsij["lj" "I" "N"] = 0.2972 * FE_vdW_coeff
epsij["lj" "I" "n"] = 0.2972 * FE_vdW_coeff
epsij["lj" "I" "O"] = 0.3323 * FE_vdW_coeff
epsij["lj" "I" "P"] = 0.3323 * FE_vdW_coeff
epsij["lj" "I" "S"] = 0.3323 * FE_vdW_coeff
epsij["lj" "I" "H"] = 0.1051 * FE_vdW_coeff
epsij["lj" "I" "f"] = 0.0743 * FE_vdW_coeff
epsij["lj" "I" "F"] = 0.2101 * FE_vdW_coeff
epsij["lj" "I" "c"] = 0.3903 * FE_vdW_coeff
epsij["lj" "I" "b"] = 0.4634 * FE_vdW_coeff
epsij["lj" "I" "I"] = 0.5520 * FE_vdW_coeff
# epsij[ "lj" "I" "M" ] = 0.6950 * FE_vdW_coeff
epsij["lj" "I" "M"] = 0.6950 * FE_vdW_coeff
epsij["lj" "I" "Z"] = 0.5510 * FE_vdW_coeff
epsij["lj" "I" "L"] = 0.5510 * FE_vdW_coeff
epsij["lj" "I" "X"] = 0.1051 * FE_vdW_coeff

epsij["lj" "M" "C"] = 0.3623 * FE_vdW_coeff
epsij["lj" "M" "N"] = 0.3742 * FE_vdW_coeff
epsij["lj" "M" "n"] = 0.3742 * FE_vdW_coeff
epsij["lj" "M" "O"] = 0.4183 * FE_vdW_coeff
epsij["lj" "M" "P"] = 0.4183 * FE_vdW_coeff
epsij["lj" "M" "S"] = 0.4183 * FE_vdW_coeff
epsij["lj" "M" "H"] = 0.1323 * FE_vdW_coeff
epsij["lj" "M" "f"] = 0.0935 * FE_vdW_coeff
epsij["lj" "M" "F"] = 0.2646 * FE_vdW_coeff
epsij["lj" "M" "c"] = 0.4914 * FE_vdW_coeff
epsij["lj" "M" "b"] = 0.5834 * FE_vdW_coeff
epsij["lj" "M" "I"] = 0.6950 * FE_vdW_coeff
epsij["lj" "M" "M"] = 0.8750 * FE_vdW_coeff
epsij["lj" "M" "Z"] = 0.6937 * FE_vdW_coeff
epsij["lj" "M" "L"] = 0.6937 * FE_vdW_coeff
epsij["lj" "M" "X"] = 0.1323 * FE_vdW_coeff

epsij["lj" "Z" "C"] = 0.2872 * FE_vdW_coeff
epsij["lj" "Z" "N"] = 0.2966 * FE_vdW_coeff
epsij["lj" "Z" "n"] = 0.2966 * FE_vdW_coeff
epsij["lj" "Z" "O"] = 0.3317 * FE_vdW_coeff
epsij["lj" "Z" "P"] = 0.3317 * FE_vdW_coeff
epsij["lj" "Z" "S"] = 0.3317 * FE_vdW_coeff
epsij["lj" "Z" "H"] = 0.1049 * FE_vdW_coeff
epsij["lj" "Z" "f"] = 0.0742 * FE_vdW_coeff
epsij["lj" "Z" "F"] = 0.2098 * FE_vdW_coeff
epsij["lj" "Z" "c"] = 0.3896 * FE_vdW_coeff
epsij["lj" "Z" "b"] = 0.4625 * FE_vdW_coeff
epsij["lj" "Z" "I"] = 0.5510 * FE_vdW_coeff
epsij["lj" "Z" "M"] = 0.6937 * FE_vdW_coeff
epsij["lj" "Z" "Z"] = 0.5500 * FE_vdW_coeff
epsij["lj" "Z" "L"] = 0.5500 * FE_vdW_coeff
epsij["lj" "Z" "X"] = 0.1049 * FE_vdW_coeff

epsij["lj" "L" "C"] = 0.2872 * FE_vdW_coeff  # these are the same as Zn values
epsij["lj" "L" "N"] = 0.2966 * FE_vdW_coeff
epsij["lj" "L" "n"] = 0.2966 * FE_vdW_coeff
epsij["lj" "L" "O"] = 0.3317 * FE_vdW_coeff
epsij["lj" "L" "P"] = 0.3317 * FE_vdW_coeff
epsij["lj" "L" "S"] = 0.3317 * FE_vdW_coeff
epsij["lj" "L" "H"] = 0.1049 * FE_vdW_coeff
epsij["lj" "L" "f"] = 0.0742 * FE_vdW_coeff
epsij["lj" "L" "F"] = 0.2098 * FE_vdW_coeff
epsij["lj" "L" "c"] = 0.3896 * FE_vdW_coeff
epsij["lj" "L" "b"] = 0.4625 * FE_vdW_coeff
epsij["lj" "L" "I"] = 0.5510 * FE_vdW_coeff
epsij["lj" "L" "M"] = 0.6937 * FE_vdW_coeff
epsij["lj" "L" "Z"] = 0.5500 * FE_vdW_coeff
epsij["lj" "L" "L"] = 0.5500 * FE_vdW_coeff
epsij["lj" "L" "X"] = 0.1049 * FE_vdW_coeff

epsij["lj" "X" "C"] = 0.0548 * FE_vdW_coeff
epsij["lj" "X" "N"] = 0.0566 * FE_vdW_coeff
epsij["lj" "X" "n"] = 0.0566 * FE_vdW_coeff
epsij["lj" "X" "O"] = 0.0632 * FE_vdW_coeff
epsij["lj" "X" "P"] = 0.0632 * FE_vdW_coeff
epsij["lj" "X" "S"] = 0.0632 * FE_vdW_coeff
epsij["lj" "X" "H"] = 0.0200 * FE_vdW_coeff
epsij["lj" "X" "f"] = 0.0141 * FE_vdW_coeff
epsij["lj" "X" "F"] = 0.0400 * FE_vdW_coeff
epsij["lj" "X" "c"] = 0.0743 * FE_vdW_coeff
epsij["lj" "X" "b"] = 0.0882 * FE_vdW_coeff
epsij["lj" "X" "I"] = 0.1051 * FE_vdW_coeff
epsij["lj" "X" "M"] = 0.1323 * FE_vdW_coeff
epsij["lj" "X" "Z"] = 0.1049 * FE_vdW_coeff
epsij["lj" "X" "L"] = 0.1049 * FE_vdW_coeff
epsij["lj" "X" "X"] = 0.0200 * FE_vdW_coeff

epsij["lj" "C" "A"] = 0.1500 * FE_vdW_coeff
epsij["lj" "A" "C"] = epsij["lj" "C" "A"]
epsij["lj" "A" "A"] = epsij["lj" "C" "C"]

epsij["lj" "A" "N"] = epsij["lj" "C" "N"]
epsij["lj" "A" "n"] = epsij["lj" "C" "n"]
epsij["lj" "A" "O"] = epsij["lj" "C" "O"]
epsij["lj" "A" "S"] = epsij["lj" "C" "S"]
epsij["lj" "A" "H"] = epsij["lj" "C" "H"]
epsij["lj" "A" "P"] = epsij["lj" "C" "P"]
epsij["lj" "A" "f"] = epsij["lj" "C" "f"]
epsij["lj" "A" "F"] = epsij["lj" "C" "F"]
epsij["lj" "A" "c"] = epsij["lj" "C" "c"]
epsij["lj" "A" "b"] = epsij["lj" "C" "b"]
epsij["lj" "A" "I"] = epsij["lj" "C" "I"]
epsij["lj" "A" "M"] = epsij["lj" "C" "M"]
epsij["lj" "A" "Z"] = epsij["lj" "C" "Z"]
epsij["lj" "A" "L"] = epsij["lj" "C" "L"]
epsij["lj" "A" "X"] = epsij["lj" "C" "X"]

epsij["lj" "N" "A"] = epsij["lj" "A" "N"]
epsij["lj" "n" "A"] = epsij["lj" "A" "n"]
epsij["lj" "O" "A"] = epsij["lj" "A" "O"]
epsij["lj" "S" "A"] = epsij["lj" "A" "S"]
epsij["lj" "H" "A"] = epsij["lj" "A" "H"]
epsij["lj" "P" "A"] = epsij["lj" "A" "P"]
epsij["lj" "f" "A"] = epsij["lj" "A" "f"]
epsij["lj" "F" "A"] = epsij["lj" "A" "F"]
epsij["lj" "c" "A"] = epsij["lj" "A" "c"]
epsij["lj" "b" "A"] = epsij["lj" "A" "b"]
epsij["lj" "I" "A"] = epsij["lj" "A" "I"]
epsij["lj" "M" "A"] = epsij["lj" "A" "M"]
epsij["lj" "Z" "A"] = epsij["lj" "A" "Z"]
epsij["lj" "L" "A"] = epsij["lj" "A" "L"]
epsij["lj" "X" "A"] = epsij["lj" "A" "X"]

#
# Hydrogen-bonding parameters
#
Rij["hb" "N" "H"] = 1.90
Rij["hb" "O" "H"] = 1.90
Rij["hb" "S" "H"] = 2.50
Rij["hb" "H" "N"] = 1.90
Rij["hb" "H" "O"] = 1.90
Rij["hb" "H" "S"] = 2.50

#
# AutoDock Binding Free Energy Model 140n
# New well-depths multiplied by the hbond.difference
# coefficient, 0.0656
#

#
# Original enthalpic well-depths for hydrogen-bonding...
#
epsij["hb" "N" "H"] = 5.0 * FE_hbond_coeff
epsij["hb" "O" "H"] = 5.0 * FE_hbond_coeff
epsij["hb" "S" "H"] = 1.0 * FE_hbond_coeff
epsij["hb" "H" "N"] = 5.0 * FE_hbond_coeff
epsij["hb" "H" "O"] = 5.0 * FE_hbond_coeff
epsij["hb" "H" "S"] = 1.0 * FE_hbond_coeff
